This repository,
excess_physician_mortality,
contains reproducible code for our open-access JAMA Internal Medicine
research letter, “Excess mortality among US physicians during the
COVID-19
pandemic”,
which uses data from the American Medical Association
(AMA)
to estimate excess mortality
among US physicians during the COVID-19 pandemic. The full citation is:
Kiang MV, Carlasare LE, Israni ST, Norcini J, Zaman JAB, Bibbins-Domingo K, Excess mortality among US physicians during the COVID-19 pandemic. JAMA Internal Medicine. 2023 Feb 6;. doi: 10.1001/jamainternmed.2022.6308. [Epub ahead of print] PubMed PMID: 36745424.
All code can be found in the ./code folder and must be run in order.
The first few lines of each code file contains a brief description of
the tasks related to that file. Numeric representation of our figures
can be found in the ./output folder. Figures are in the ./plots
folder. Tables are generated using rmarkdown and both source and
output are in the ./rmds folder. Where applicable, the (shareable) raw
data are in ./data_raw and the (shareable) processed data are in the
./data folder.
- Mathew V Kiang
(
: mkiang |
: @mathewkiang)
- Lindsey E Carlasare
- Sonoo Thadaney Israni
- John J Norcini
- Junaid AB Zaman
- Kirsten
Bibbins-Domingo
(
This study was not directly funded. LEC is employed by the American Medical Association (AMA). STI serves on the boards of UNICEF Northwestern Region, SCIENTS, and Society of Bedside Medicine in an unpaid capacity. KBD is editor-in-chief of JAMA and the JAMA Network. MVK is supported by the National Institutes of Health for work outside the scope of this manuscript. No individuals received compensation outside of their usual salaries for their contributions to this work. No other conflicts to report. See the full manuscript for all acknowledgements, conflicts, and disclaimers.
The AMA, NIH, and other institutions listed above had no role in the design and conduct of the study, nor the decision to prepare and submit the manuscript for publication.
Note, due to limitations in our data use agreement, we cannot share physician data (see online Supplement 2). However, we provide reproducible code here such that researchers who have access to the AMA Masterfile and corresponding AMA Deceased Physician File can reproduce and extend our results.
We use renv for package
management but below we also post the relevant session information to
ensure full reproducibility.
> sessioninfo::session_info()
─ Session info ─────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os macOS Monterey 12.6.1
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2022-11-11
rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
─ Packages ─────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
anytime 0.3.9 2020-08-27 [1] CRAN (R 4.2.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
broom 1.0.1 2022-08-29 [1] CRAN (R 4.2.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.2.0)
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.0)
P codetools 0.2-18 2020-11-04 [?] CRAN (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
config * 0.3.1 2020-12-17 [1] CRAN (R 4.2.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0)
curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.2.0)
digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.0)
distributional 0.3.1 2022-09-02 [1] CRAN (R 4.2.0)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.0)
excessmort * 0.6.3 2022-11-11 [1] Github (rafalab/excessmort@571a5b7)
fable * 0.3.2 2022-09-01 [1] CRAN (R 4.2.0)
fabletools * 0.3.2 2021-11-29 [1] CRAN (R 4.2.0)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
feasts * 0.3.0 2022-09-01 [1] CRAN (R 4.2.0)
forcats * 0.5.2 2022-08-19 [1] CRAN (R 4.2.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.0)
forecast * 8.18 2022-10-02 [1] CRAN (R 4.2.0)
fracdiff 1.5-2 2022-10-31 [1] CRAN (R 4.2.0)
fs * 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
furrr * 0.3.1 2022-08-15 [1] CRAN (R 4.2.0)
future * 1.29.0 2022-11-06 [1] CRAN (R 4.2.0)
future.apply * 1.10.0 2022-11-05 [1] CRAN (R 4.2.0)
gargle 1.2.1 2022-09-08 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.0)
ggstance 0.3.5 2020-12-17 [1] CRAN (R 4.2.0)
globals 0.16.1 2022-08-28 [1] CRAN (R 4.2.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
googledrive 2.0.0 2021-07-08 [1] CRAN (R 4.2.0)
googlesheets4 1.0.1 2022-08-13 [1] CRAN (R 4.2.0)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
haven 2.5.1 2022-08-22 [1] CRAN (R 4.2.0)
here * 1.0.1 2020-12-13 [1] CRAN (R 4.2.0)
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.0)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.0)
janitor * 2.1.0 2021-01-05 [1] CRAN (R 4.2.0)
jsonlite 1.8.3 2022-10-21 [1] CRAN (R 4.2.0)
knitr 1.40 2022-08-24 [1] CRAN (R 4.2.0)
P lattice 0.20-45 2021-09-22 [?] CRAN (R 4.2.1)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.2.0)
lubridate * 1.9.0 2022-11-06 [1] CRAN (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
modelr 0.1.10 2022-11-11 [1] CRAN (R 4.2.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
P nlme 3.1-157 2022-03-25 [?] CRAN (R 4.2.1)
P nnet 7.3-17 2022-01-16 [?] CRAN (R 4.2.1)
parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
purrr * 0.3.5 2022-10-06 [1] CRAN (R 4.2.0)
quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.2.0)
quantmod 0.4.20 2022-04-29 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0)
readr * 2.1.3 2022-10-01 [1] CRAN (R 4.2.0)
readxl 1.4.1 2022-08-17 [1] CRAN (R 4.2.0)
renv 0.16.0 2022-09-29 [1] CRAN (R 4.2.0)
reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.0)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
rvest 1.0.3 2022-08-19 [1] CRAN (R 4.2.0)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
snakecase 0.11.0 2019-05-25 [1] CRAN (R 4.2.0)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0)
stringr * 1.4.1 2022-08-20 [1] CRAN (R 4.2.0)
tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
tidyr * 1.2.1 2022-09-08 [1] CRAN (R 4.2.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
tidyverse * 1.3.2 2022-07-18 [1] CRAN (R 4.2.0)
timechange * 0.1.1 2022-11-04 [1] CRAN (R 4.2.0)
timeDate 4021.106 2022-09-30 [1] CRAN (R 4.2.0)
tseries 0.10-52 2022-10-10 [1] CRAN (R 4.2.0)
tsibble * 1.1.3 2022-10-09 [1] CRAN (R 4.2.0)
TTR 0.24.3 2021-12-12 [1] CRAN (R 4.2.0)
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
urca 1.3-3 2022-08-29 [1] CRAN (R 4.2.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.2.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
xfun 0.34 2022-10-18 [1] CRAN (R 4.2.0)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
xts 0.12.2 2022-10-16 [1] CRAN (R 4.2.0)
yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.0)
zoo 1.8-11 2022-09-17 [1] CRAN (R 4.2.0)
P ── Loaded and on-disk path mismatch.
────────────────────────────────────────────────────────────────────────────────> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices datasets utils methods base
other attached packages:
[1] config_0.3.1 tsibble_1.1.3 future.apply_1.10.0 feasts_0.3.0
[5] fable_0.3.2 fabletools_0.3.2 forecast_8.18 lubridate_1.9.0
[9] timechange_0.1.1 janitor_2.1.0 fs_1.5.2 furrr_0.3.1
[13] future_1.29.0 excessmort_0.6.3 here_1.0.1 forcats_0.5.2
[17] stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5 readr_2.1.3
[21] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] nlme_3.1-157 xts_0.12.2 doParallel_1.0.17 httr_1.4.4
[5] rprojroot_2.0.3 tools_4.2.1 backports_1.4.1 utf8_1.2.2
[9] R6_2.5.1 DBI_1.1.3 colorspace_2.0-3 nnet_7.3-17
[13] withr_2.5.0 tidyselect_1.2.0 curl_4.3.3 compiler_4.2.1
[17] cli_3.4.1 rvest_1.0.3 xml2_1.3.3 tseries_0.10-52
[21] scales_1.2.1 lmtest_0.9-40 fracdiff_1.5-2 quadprog_1.5-8
[25] digest_0.6.30 rmarkdown_2.18 pkgconfig_2.0.3 htmltools_0.5.3
[29] sessioninfo_1.2.2 parallelly_1.32.1 dbplyr_2.2.1 fastmap_1.1.0
[33] TTR_0.24.3 rlang_1.0.6 readxl_1.4.1 quantmod_0.4.20
[37] rstudioapi_0.14 farver_2.1.1 generics_0.1.3 zoo_1.8-11
[41] jsonlite_1.8.3 googlesheets4_1.0.1 distributional_0.3.1 magrittr_2.0.3
[45] Rcpp_1.0.9 munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.3
[49] stringi_1.7.8 yaml_2.3.6 snakecase_0.11.0 ggstance_0.3.5
[53] grid_4.2.1 listenv_0.8.0 crayon_1.5.2 lattice_0.20-45
[57] haven_2.5.1 hms_1.1.2 knitr_1.40 anytime_0.3.9
[61] pillar_1.8.1 codetools_0.2-18 urca_1.3-3 reprex_2.0.2
[65] glue_1.6.2 evaluate_0.18 renv_0.16.0 modelr_0.1.10
[69] vctrs_0.5.0 tzdb_0.3.0 foreach_1.5.2 cellranger_1.1.0
[73] gtable_0.3.1 assertthat_0.2.1 xfun_0.34 broom_1.0.1
[77] googledrive_2.0.0 timeDate_4021.106 gargle_1.2.1 iterators_1.0.14
[81] globals_0.16.1 ellipsis_0.3.2